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Item Honey bee host-virus interactions at the individual and cellular level(Montana State University - Bozeman, College of Agriculture, 2021) McMenamin, Alexander James; Chairperson, Graduate Committee: Michelle Flenniken; This is a manuscript style paper that includes co-authored chapters.Honey bees are important pollinators of the fruits, nuts and vegetable crops that feed our growing population. Unfortunately, honey bee colony losses have averaged 38% from 2008-2018. These losses are due to a variety of factors, including reduced quality forage, pesticide exposure in agricultural fields, parasites like the Varroa destructor mite, and pathogens. The most diverse group of pathogens effecting honey bees are small RNA viruses. Honey bees have evolved numerous strategies to restrict virus infection, including the RNA interference (RNAi) pathway. Bees infected with a model virus, Sindbis-GFP (SINV) have differential expression of hundreds of genes, including RNAi genes and several heat shock protein (HSP) encoding genes. Therefore, we hypothesized that heat shock proteins are antiviral in honey bees. To induce the heat shock response (HSR), SINV-infected bees were heat shocked at 42°C for 4 hours. Heat shock resulted in a 74-90% reduction in SINV RNA copies as compared to bees maintained at 32°C. Heat shocked and/or virus-infected bees had increased expression of several core HSR protein-encoding genes, but heat shock did not consistently result in the increased expression of RNAi genes (argonaute-2 and dcr-like). This indicates that heat shock proteins are contributing to an antiviral response. SINV-infected bees also had higher expression of a recently identified antiviral gene - bee antiviral protein-1 (bap1). Therefore, we further characterized bap1 using computation approaches including phylogenetic analysis, which determined that this gene is taxonomically restricted to Hymenoptera and Blatella germanica (the German cockroach). Structural predication programs indicated that bap1 is a highly disordered protein. Intriguingly, transcriptome and correlation analyses determined that bap1 was coexpressed with several genes implicated in antiviral immunity (i.e., ago2, tudor-sn and TEP7). Although the precise antiviral function of bap1 remains to be elucidated, we further developed experimental tools that will enable more incisive investigation of bap1 and other antiviral genes. Primary cultures of larval hemocytes (immune cells) and mixed-cell pupal tissue cultures supported productive replication of sacbrood virus, deformed wing virus, and Flock House virus. Infected pupal cell cultures exhibited virus-specific transcriptional responses in bap1, ago2, and dcr-like expression. Together, these data further elucidate honey bee antiviral immunity and provide new tools for studying honey bee host-virus interactions.