Data from: Interactions of husbandry, landscape, and immunity in regulating viral loads for managed honey bees
Data files
Sep 19, 2025 version files 149.13 KB
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AllData.xlsx
142.31 KB
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HiveSummary.csv
2.98 KB
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README.md
3.84 KB
Abstract
The western honey bee, Apis mellifera, continues to experience widespread die-offs that threaten their critical ecological and agricultural roles. Given the recognized impact of viruses on the increased mortality rates, it is imperative to understand the forces shaping viral infections. In this study, we explore how hive husbandry, landscape, and immunity influence viral loads in managed bees. We characterized 43 apiaries across Central Florida for eight husbandry interventions, five landscape variables, transcription of four immune genes, and infection intensities of four viruses: Black Queen Cell Virus (BQCV), Deformed Wing Virus (DWV-A), Lake Sinai Virus (LSV-2), and Israeli Acute Paralysis Virus (IAPV). We found that colonies surrounded by more floral resources and fresh water bodies were associated with increased viral loads and increased viral coinfections. We speculate that increased floral resources increased pollinator abundance, thereby increasing transmission rates and viral richness. We further speculate that increased open water similarly increased pollinator abundance and/or exposure to immunity-altering pesticides. Last, we show that husbandry interventions aimed at reducing Varroa destructor mites can have positive and negative off-target viral impacts. Our data underscore the importance of landscape, immunity, and husbandry in honey bee disease dynamics and highlight the complexity of their interactions.
Dataset DOI: 10.5061/dryad.j6q573nt5
Description of the data and file structure
This file includes individual-level data on viral load, immune gene expression, husbandry practices, and landscape characteristics.
Files and variables
File: AllData.xlsx
Description: This file includes individual-level data on viral load, immune gene expression, husbandry practices, and landscape characteristics.
Notes:
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Each sample underwent qPCR twice: once for viral assays and once for immune gene assays. Both assays used Actin as a reference gene, resulting in two separate Actin Cq values (Act_ct and Act_cq).
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For final modeling, Actin Cq values were averaged.
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Samples with missing immune gene data are included but were excluded from relevant statistical models. Missing values are indicated by blank cells.
Variable Codes:
Husbandry Variables ( 0 = treatment not applied; 1 = treatment applied)
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SF = supplemental feeding usage
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SHB = Small Hive Beetle prevention usage
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EO = essential oil usage
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Api = Apiguard usage
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Ami = amitraz usage
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Hops = hops usage
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OA = oxalic acid usage
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FA = formic acid usage
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Miticides = general usage of miticides (umbrella term)
Landscape Variables (Values represent proportions within a 2 km radius. A +1 was added to zero values for later log transformations.)
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BFA = Bee Forage Area
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IS = Impervious Surfaces
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NL = Natural Lands
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Ag = Agriculture
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OW = Open Water (fresh)
Immunity Variables:
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Act_cq: Actin Cq value for immune assays
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PPO_cq, Def_cq, Dom_cq, Dic_cq: Raw Cq values for PPO, Defensin, Domeless, and Dicer
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dPPO, dDef, dDom, dDicer: ΔCq = Immune gene Cq – Actin Cq
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CN_PPO, CN_Def, CN_Dom, CN_Dic: Calculated copy number (methods in manuscript)
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PPO, Def, Dome, Dicer: log₁₀-transformed copy numbers
Viral Variables:
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Act_ct: Actin Cq value for viral assays
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BQCV_ct, DWV_ct, IAPV_ct, LSV_ct: Raw viral Cq values
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dBQCV, dDWV, dIAPV, dLSV: ΔCq = Viral gene Cq – Actin Cq
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CN_BQCV, CN_DWV, CN_IAPV, CN_LSV: Viral copy numbers
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BQCV, DWV, IAPV, LSV: log₁₀-transformed viral copy numbers
Principal Components & Other Calculated Metrics:
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PC_virus, PC_virusR: Principal component scores summarizing viral load
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PC_imm: Principal component of immune gene expression
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PC_land: Principal component of landscape characteristics
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PC_hus: Principal component of husbandry variables
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Viral_rich: Number of detected viruses per sample
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Viral_cat: Categorical variable summarizing viral co-infection status. Values are represented by single-letter codes (one or more letters may appear if multiple viruses were detected). D= Deformed Wing Virus; B= Black Queen Cell Virus; I = Israeli Acute Paralysis Virus; L= Lake Sinai Virus.
File: HiveSummary.csv
Description: This file includes colony-level averages of viral infection and associated environmental variables.
Variable Codes:
Husbandry Variables ( 0 = treatment not applied; 1 = treatment applied)
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SF = supplemental feeding usage
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SHB = Small Hive Beetle prevention usage
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EO = essential oil usage
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Api = Apiguard usage
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Ami = amitraz usage
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Hops = hops usage
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OA = oxalic acid usage
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FA = formic acid usage
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Miticides = general usage of miticides (umbrella term)
Landscape Variables (Values represent proportions within a 2 km radius. A +1 was added to zero values for later log transformations.)
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BFA = Bee Forage Area
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IS = Impervious Surfaces
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NL = Natural Lands
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Ag = Agriculture
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OW = Open Water (fresh)
Viral Load (Colony Averages):
- Log(BQCV), Log(DWV), Log(IAPV), Log(LSV): Log-transformed mean viral copy number per colony