Viruses are omnipresent, yet the knowledge on drivers of viral prevalence in wild host populations is often limited. Biotic factors, such as sympatric managed host species, as well as abiotic factors, such as climatic variables, are likely to impact viral prevalence. Managed and wild bees, which harbor several multi-host viruses with a mostly fecal–oral between-species transmission route, provide an excellent system with which to test for the impact of biotic and abiotic factors on viral prevalence in wild host populations. Here we show on a continental scale that the prevalence of three broad host viruses: the AKI-complex (Acute bee paralysis virus, Kashmir bee virus and Israeli acute paralysis virus), Deformed wing virus, and Slow bee paralysis virus in wild bee populations (bumble bees and solitary bees) is positively related to viral prevalence of sympatric honey bees as well as being impacted by climatic variables. The former highlights the need for good beekeeping practices, including Varroa destructor management to reduce honey bee viral infection and hive placement. Furthermore, we found that viral prevalence in wild bees is at its lowest at the extreme ends of both temperature and precipitation ranges. Under predicted climate change, the frequency of extremes in precipitation and temperature will continue to increase and may hence impact viral prevalence in wild bee communities.

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This protocol was developed for the COST-Action “Super-B”, whose purpose was to coordinate research, outreach and policy towards sustainable pollination1-3. The protocol addresses the detection of parasites and pathogens across bee species, as one of several possible drivers of bee decline4,5. It consists of four major components:1. A sample collecting protocol, based around a dominant bee species driving pathogen distribution among other bee species2. A sample processing protocol, based on analyzing nucleic acids from individual bees3. A pathogen detection protocol, based on RT-qPCR with broad-range primers for several common pathogens4. A barcoding protocol, for accurate bee species identification The protocols have largely been adapted from existing knowledge and protocols but also include two key innovations: the use of passive reference nucleic acids and synthetic positive controls, that significantly improve the quality and robustness of the raw data, and thus the reliability of the analyses and conclusions.