Sacbrood viruses and select Lake Sinai virus variants dominated Apis mellifera colonies symptomatic for European foulbrood

European foulbrood (EFB) is a prevalent disease of the European honey bee (Apis mellifera) in the US, which can lead to colony decline and collapse. The bacterial components of EFB are well studied, but the diversity of viral infections within infected colonies has not been explored. Here we use meta-transcriptomics sequencing of 12 honey bee hives, symptomatic (+) and asymptomatic (-) for EFB to explore viral infection associated with the disease. We identified 41 viral genomes, belonging to two families, with a predominant occurrence of 34 genomes observed in colonies with severe EFB. This is in contrast to fewer, and a complete absence of Dicistroviridae genomes, recovered from healthy colonies (7 genomes). Identified viruses included multiple lineages previously reported in honey bees, namely Lake Sinai virus, Deformed wing virus, Sacbrood virus, Black queen cell virus, and Israeli acute paralysis virus. We observed specific Lake Sinai virus clades associated exclusively with EFB+ or EFB-colonies, in addition to EFB-afflicted colonies that exhibited an increase in relative abundance of sacbrood viruses. Multivariant analyses highlighted that a combination of site and EFB disease status influenced RNA virome composition, while EFB status alone didnt significantly impact it, presenting a challenge for comparisons between colonies kept in different yards. These findings contribute to the understanding of viral dynamics in honey bee colonies compromised by EFB and underscore the need for future investigations to consider viral composition when investigating EFB. ImportanceThis study on the viromes of honey bee colonies affected by European foulbrood (EFB) sheds light on the dynamics of viral populations in bee colonies in the context of a prevalent bacterial brood disease. The identification of distinct Lake Sinai virus and Sacbrood virus clades associated with colonies with severe EFB suggests a potential connection between viral composition and disease status, emphasizing the need for further investigation into the role of viruses during EFB infection. The observed increase in sacbrood viruses during EFB infection implies a possible viral dysbiosis, with potential implications for honey bee brood health. These findings contribute valuable insights for apicultural practices, offering a foundation for future research aimed at understanding and mitigating the impact of bacterial and viral infection in commercial honey bee operations and the management of EFB.