Molecular diagnostics have revolutionized disease detection and pathogen characterization. Next-generation sequencing allows for high-throughput analysis of samples and has advanced our understanding of viruses. Deformed wing virus of honeybees exists as a quasispecies with different strains exhibiting varying virulence. Exposure to Varroa mites has increased the prevalence and diversity of DWV strains worldwide over the past few decades, contributing to honeybee population declines. Continued development of molecular techniques will further our knowledge of pathogen evolution and improve disease management.