Primers, site data, and virus abundance in honey bees and Andrena spp.
Data files
Aug 26, 2025 version files 314.08 KB
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README.md
5.01 KB
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Standard_curve_AmFV.jpeg
128.31 KB
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Standard_curve_BQCV.jpeg
38.53 KB
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Standard_curve_DWV.jpeg
34.65 KB
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Standard_curve_LSV2.jpeg
35.42 KB
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Standard_curve_SBV.jpeg
31.48 KB
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T1._Primers.xlsx
9.68 KB
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T2._Sites.xlsx
12.46 KB
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T3._qPCR-_Andrena_sample.csv
8.28 KB
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T4._qPCR-_Apis_mellifera_sample.csv
10.25 KB
Abstract
Bees are focal pollinators, essential for maintaining biodiversity and crop production. Thus, reports of high annual honey bee colony losses and population declines among many wild bees in different parts of the world are of major concern. The spread of viruses is highlighted as a potential threat to bee communities. Viruses infect a wide range of bee species, and can be transmitted interspecifically through shared floral resources. Therefore, the role of flowers as hubs of bee virus transmission requires a community ecology perspective. Here, we investigate local and landscape-scale characteristics of floral communities potentially associated with the spread of viruses in the solitary Andrena spp. (mining bees). We surveyed 14 sites in a Mediterranean agroecosystem with varying local densities of honey bee (Apis mellifera) foragers and diversity of flowering species, and assessed the prevalence of four common Hymenoptera-associated viruses [deformed wing virus (DWV), black queen cell virus (BQCV), sacbrood virus (SBV) and Lake Sinai virus-2 (LSV2)] in co-foraging honey bees and mining bees. We found that the probability of virus presence in mining bees was generally associated with the diversity and composition of the local (site level) floral community, and with floral resource availability at the landscape scale (up to 1000 m range). In addition, SBV and DWV prevalence in mining bees was positively related to the density of SBV-infected, and total honey bee foragers, respectively. These findings demonstrate the focal role that the floral community at multiple spatial scales, and co-foraging pollinator species, may play in virus spread and, potentially, pollinator health.
https://doi.org/10.5061/dryad.crjdfn3df
Description of the data and files structure
The dataset includes the following four tables:
T1. Primers
Lists the primers used in the qPCR assay for viral screening of the sampled bees. For each primer, the following attributes are specified: purpose, primer name, sequence (5’-3’), product size (bp), and reference.
T2. Sites
Contains detailed information on each surveyed site, including the following attributes: floral species richness (flowering plants visited by bees) as recorded during the survey, floral diversity (Shannon index), Floral Resource Availability (FRA) index computed based on land cover data, coordinates (UTM) of each site, forager density of Apis mellifera and Andrena (bees per 40 minutes), analysis sample size for each Apis mellifera and Andrena forager for each of the four viruses (BQCV, DWV, LSV, SBV), and the prevalence of each virus in Apis mellifera and Andrena.
The site coordinates are reported at full collected precision to enable spatial analyses. The focal Andrena species studied are common and widespread in the region, thrive in disturbed habitats, and are not listed as threatened, endangered, or vulnerable in global or regional assessments. Therefore, publishing precise coordinates is not expected to pose a conservation risk.
T3. qPCR- Andrena sample
Presents data on virus abundance in individual Andrena samples for viruses identified in the preceding Next Generation Sequencing (NGS) assay conducted on pooled bee sub-samples (Daughenbaugh et al. 2021). This includes the four focal viruses - BQCV, DWV, SBV, LSV - and an additional, less prevalent virus, AmFV. Virus abundance in individual bee samples was assessed using qPCR, with viral RNA copy numbers calculated from a standard curve and expressed as the number of viral RNA copies per 100 ng of RNA. For statistical analyses, quantitative data were reduced to presence (1) or absence (0). In the table, "specimen.number" identifies each bee in the sample, "qPCR.batch" refers to the qPCR run (1–3), and "Genus" and "Species" indicate taxonomic classification. The standard curves for each of the five viruses are presented in separate files.
T4. qPCR- Apis mellifera sample
Virus abundance in individual honey bee (Apis mellifera) samples. Column names and descriptions are as described under "T3. qPCR- Andrena sample". NAs (not available) indicate cases where there was insufficient RNA left to generate cDNA for viral RNA quantification by qPCR. The standard curves for each of the five viruses are presented in separate files.
Contact
In case of questions regarding this data file, users may contact Idan Kahnonitch at idan.kanonitch@mail.huji.ac.il.
Files and variables
Files:
T1._Primers.xlsx
T2._Sites.xlsx
T3._qPCR-_Andrena_sample.csv
T4._qPCR-_Apis_mellifera_sample.csv
Standard_curve_BQCV.jpeg
Standard_curve_DWV.jpeg
Standard_curve_SBV.jpeg
Standard_curve_LSV2.jpeg
Standard_curve_AmFV.jpeg
Description:
This dataset consists of four tables, each presented in a separate Excel file, and five image plots. It contains the following information:
- Details of primers used in qPCR assays (T1. Primers).
- Surveyed sites with key attributes (T2. Sites).
- Virus abundance data for Andrena (T3. qPCR – Andrena sample).
- Virus abundance data for Apis mellifera (T4. qPCR – Apis mellifera sample)
- qPCR standard curve plot for BQCV (Black queen cell virus), used to calculate viral RNA copy numbers in individual bee samples (Standard_curve_BQCV)
- qPCR standard curve plot for DWV (Deformed wing virus), used to calculate viral RNA copy numbers in individual bee samples (Standard_curve_DWV)
- qPCR standard curve plot for LSV2 (Lake Sinai virus 2), used to calculate viral RNA copy numbers in individual bee samples (Standard_curve_LSV2)
- qPCR standard curve plot for SBV (Sacbrood virus), used to calculate viral RNA copy numbers in individual bee samples (Standard_curve_SBV)
- qPCR standard curve plot for AmFV (Apis mellifera filamentous virus), used to calculate viral RNA copy numbers in individual bee samples (Standard_curve_AmFV)
Code/software
The dataset tables were created in Microsoft Excel (XLSX and CSV) and can be viewed using many free or widely available programs, including:
- Google Sheets
- Chrome extension “Office Editing”
- LibreOffice Calc
- Apache OpenOffice
- Aspose Excel Viewer
- Zoho Sheet
The standard curve plots are provided as image files (JPEG) and can be viewed with common free programs, such as:
- Windows Photos (Windows)
- Preview (Mac)
- ImageJ (cross-platform, open source)
- GIMP (cross-platform, open source)
We conducted a field survey during spring 2018, which included a total of fourteen sites. Each site comprised a 625 m2 plot located at the center of a larger wild bloom patch (mostly >3000m2). Field work was conducted in mid-March, corresponding to peak spring bloom, and lasted two weeks. Each site was sampled once between 8:00 and 16:00 when weather conditions were favorable for bee activity (temperature >17 °C, wind velocity <3 m/s, and clear or partially clear skies). Foraging bee sampling was carried out for a total of 40 person-minutes (excluding handling time of captured bees) and conducted by slowly walking throughout the plot and hand-netting any bee that was observed landing on a flower, while keeping records of the visited flower species. Each captured bee was identified in-situ to the lowest taxonomic level possible, immediately placed in a vial, and kept on dry ice. We collected additional foraging bees as needed to attain a sample of at least 11 Andrena and 11 A. mellifera individuals per site for viral screening. At the end of each sampling day, all the collected specimens were brought to the lab and stored at –80 °C. The sample of mining bees that was used for viral screening consisted of the three most dominant Andrena species (collectively comprising > 70% of the observed Andrena individuals in the study): A. ocraceohirta, A. aerinifrons levantina, A. urfanella, and a closely related morphospecies from the subgenus Truncandrena. From each site, virus identification efforts were focused on individual A. mellifera and Andrena (median=11). High throughput sequencing identified regional virus genome sequence variations for BQCV and LSV-2, which required utilization of new primer sequences (Daughenbaugh et al., 2021). The presence and abundance of four common hymenopteran viruses, namely BQCV, DWV, SBV, and LSV-2, was assessed using the procedure of RNA extraction followed by cDNA preparation, polymerase chain reaction (PCR) and qPCR, as described in Daughenbaugh et al. (2021).
