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Fig. S1. Estimated LD50 of BQCV concentration on larval honey bees calculated from a linear mixed model using colony as random effect. The estimated LD50 is 1.53 × 108 genome equivalents (95% CI = 6.99 × 107/ 1.35 × 109) at 11 days post-infection. Linear regression: R2 = 0.714.

Fig. S2. Mean sugar consumption per bee and per day (± SEM) for treatments with and without pesticide during Experiment 3 (N. ceranae, BQCV and thiacloprid). Presence of thiacloprid had a negative effect on sugar consumption (linear mixed model using colony as random effect; t = −3.998, df = 18, P < 0.001), while infection with pathogens did not: N. ceranae (t = −1.042, df = 18, P = 0.3114) and BQCV (t = −1.833, df = 18, P = 0.0834). The decrease in sugar consumption due to the presence of thiacloprid in the food is of the order of 15% (calculated from the median values of sugar consumption for both groups, without (40.1 μl/bee/day) and with thiacloprid (34.0 μl/bee/day). The green line represents the sugar consumption of honey bees from the treatments without thiacloprid, and the blue line represents the mean consumption of honey bees from the treatments with thiacloprid. Thiacloprid was mixed into the 50% sucrose solution (0.1% acetone) provided ab libitum to honey bee workers across the whole experiment.

Fig. S3. Estimated LD50 following chronic exposure of larval honey bees to thiacloprid, calculated from a linear mixed model using colony as random effect. The estimated LD50 is 76.9 mg/kg thiacloprid (95% CI 60.5/99.8), 7 days after the first ingestion. Linear regression: R2 = 0.913.

Fig. S4. Design of the three experiments.

Table S1. Instantaneous risk of death (hazard ratio, ± 95% CI) for adult honey bees in each treatment of Experiment 2 (N. ceranae and BQCV) compared with the control treatment, calculated from a Cox proportional hazard mixed model using treatment as fixed effect and colony and cages as nested random effects. In bold are the treatments with a hazard ratio statistically different to the control treatment.

Table S2. Instantaneous risk of death (hazard ratio, ± 95% CI) for adult honey bees in each treatment of Experiment 3 (N. ceranae, BQCV and thiacloprid) compared with the control treatment, calculated from a Cox proportional hazard mixed model using treatment as fixed effect and colony and cages as nested random effects. In bold are the treatments with a hazard ratio statistically different to the control treatment.

Table S3. Coefficient contrast comparisons, adjusted (or not) for multiple comparisons with FDR method based on the hazard ratio from each treatment in Experiment 3 (N. ceranae, BQCV and thiacloprid). Double treatments were compared with single treatments, while the triple treatment (N. ceranae + BQCV + thiacloprid) was compared with the three doublet treatments. In bold is the comparison that appeared significant without correction for multiple analyses.

Table S4. List of primers used for quantification of viruses after propagation, using RT-qPCR (and efficiency of qPCR). The qPCR efficiency for BQCV quantification after experimental infections in adults and larvae was of 103.3%.

Appendix S1. Effect of chronic exposure to a sublethal dose of thiacloprid (0.1 mg/kg) and three different doses of BQCV, alone or in combination, on larval honey bee mortality.

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