Contrasts in honey-bee pathogen abundance by colony status.

The difference in mean ΔCT values (normalized threshold cycle in qPCR reactions) was compared by ANOVA for two non-independent contrasts: all CCD colonies (n = 61) versus all non-CCD colonies (n = 63), and weak (n = 15) versus strong (n = 29) colonies in non-CCD apiaries. Weak colonies had six or fewer frames of bees and strong colonies had seven or more frames (see Materials and Methods). Non-CCD colonies include both sympatric and allopatric colonies, which were combined for increased statistical power. ΔΔ is the mean Δof the non-CCD population minus the mean Δvalue of the CCD population. Thus, positive numbers represent a decrease in mean threshold cycle and an increase in pathogen abundance. Fold change between categories is calculated as (1+ primer efficiency) ΔΔCT. SE = standard error of population mean ΔCT; P-value = probability of equal mean ΔCT by ANOVA (i.e., that the true ΔΔCT = 0); ABPV = acute bee paralysis virus; DWV = deformed wing virus; SBV = sacbrood virus; BQCV = black queen cell virus; IAPV = Israeli acute paralysis virus; KBV = Kashmir bee virus.