Understanding the ecological and evolutionary processes that drive host-pathogen interactions is critical for combating epidemics and conserving species. The Varroa destructor mite and deformed wing virus (DWV) are two synergistic threats to Western honey bee (Apis mellifera) populations across the globe. Distinct honey bee populations have been found to self-sustain despite Varroa infestations, including colonies within the Arnot Forest outside Ithaca, NY, USA. We hypothesized that in these bee populations, DWV has been selected to produce an avirulent infection phenotype, allowing for the persistence of both host and disease-causing agents. To investigate this, we assessed the titer of viruses in bees from the Arnot Forest and managed apiaries, and assessed genomic variation and virulence differences between DWV isolates. Across groups, we found viral abundance was similar, but DWV genotypes were distinct. We also found that infections with isolates from the Arnot Forest resulted in higher survival and lower rates of symptomatic deformed wings, compared to analogous isolates from managed colonies, providing preliminary evidence to support the hypothesis of adaptive decreased viral virulence. Overall, this multi-level investigation of virus genotype and phenotype across different contexts reveals critical insight into global bee health and the ecological and evolutionary processes driving host-pathogen interactions.

Spreadsheet contains data collected from naturally infected honey bee samples (Table 1-14) and experimental infections (Table 15-31). Description of each sheet can be found in Metadata sheet. The two R files contain code for analyzing the natural infections (Arnot_1.R) and experimental infections (Arnot_2.R). Basic pipeline for sequence analysis can be found in Arnot_seq_code.txt file. Consensus genomes, as well as raw sequence reads, can be found on the NCBI Genome and SRA database (PRJNA922567 and PRJNA922218, genome accessions OR497372-OR497398).

Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1645331 Funding provided by: U.S. Department of AgricultureCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000199Award Number: 2021-67011-35115 Funding provided by: U.S. Department of AgricultureCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000199Award Number: GNE19-214-33243