-The US National Honey Bee Disease Survey sampled colony pests and diseases from 2009 to 2014. We verified the absence of Tropilaelaps spp., the Asian honey bee (Apis cerana ), and slow bee paralysis virus. Endemic health threats were quantified, including Varroa destructor , Nosema spp., and eight honey bee viruses. Varroa loads varied across years, with annual fall peaks; Nosema peaked January to April. Migratory beekeepers had significantly lower Varroa prevalence (84.9 vs. 97.0 %) and loads (3.65 ± 0.28 vs. 5.99 ± 0.22) than stationary operations, while Nosema was more prevalent (59.9 vs. 46.7 %) in migratory colonies. Since 2010, chronic bee paralysis virus prevalence doubled annually. We detected strong positive relationships between V. destructor and Varroa -transmitted viruses, between Nosema and Lake Sinai virus 2, and a positive relationship across several viral pathogens of bees. The results provide a disease baseline to help identify drivers of poor bee health.Apis mellifera / disease survey / pests / parasite / USA

RNA viruses impact honey bee health and contribute to elevated colony loss rates worldwide. Deformed wing virus (DWV) and the closely related Varroa destructor virus-1 (VDV1), are the most widespread honey bee viruses. VDV1 is known to cause high rates of overwintering colony losses in Europe, however it was unknown in the United States (US). Using next generation sequencing, we identified VDV1 in honey bee pupae in the US. We tested 603 apiaries the US in 2016 and found that VDV1 was present in 66.0% of them, making it the second most prevalent virus after DWV, which was present in 89.4% of the colonies. VDV1 had the highest load in infected bees (7.45*1012 ± 1.62*1012 average copy number ± standard error) compared to other tested viruses, with DWV second (1.04*1012 ± 0.53*1012). Analysis of 75 colonies sourced in 2010 revealed that VDV1 was present in only 2 colonies (2.7%), suggesting its recent spread. We also detected newly emerged recombinants between the US strains of VDV1 and DWV. The presence of these recombinants poses additional risk, because similar VDV1-DWV recombinants constitute the most virulent honeybee viruses in the UK.

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The honey bee Apis mellifera L. colony is headed by a single and indispensable queen, whose duty it is to ensure brood production and provide pheromonal stability within the colony. This study presents a non-invasive method that allows the identification of the queen maternal lineage and subspecies using the remaining tissue of her clipped wing. The DraI mtDNA COI-COII (DmCC) test was applied to various sizes of queen and worker wings and the results were compared with data obtained from other bee tissues. Furthermore, we propose a new method allowing in silico transition of the DmCC test and haplotype identification based on extended sequencing of the tRNAleu and COII genes. Our results show that DNA extracted by Chelex 10% from one-third of a queen’s wing is deemed adequate for a successful identification of her maternal evolutionary lineage, haplotype and subspecies. The in silico method proposed in this study fully adheres to the established guidelines of the DmCC, provides a universal standard for haplotype identification, and offers faster and more precise results by reconciling both cleaved amplified polymorphic sequences (CAPS) and Sanger sequencing approaches.