Honey Bee Viromes from Beekeeping Operations Experiencing High Losses in 2022–2023

Recent high annual losses of honey bee (<i>Apis mellifera</i>) colonies, averaging 40% in the United States from 2008 to 2025, are concerning for beekeepers, growers, policy makers, and scientists. Viruses, the most abundant group of honey bee pathogens, impact honey bee fitness and contribute to colony losses. Several studies have utilized next-generation sequencing (NGS) technologies to discover new honey beeinfecting viruses and expand our understanding of the honey bee virome. Herein, we examined the viromes of honey bees obtained from longitudinally monitored, commercially managed colonies that experienced population decline (average ~44%) during the 2022-2023 beekeeping season. We hypothesized new viruses or virus genome variants may be associated with these declines. To test this hypothesis, we sequenced RNA obtained from virus-augmented honey bee samples from representative colonies managed by four beekeeping operations in California. We discovered three undescribed partitivirus-like sequences that were prevalent and abundant in all beekeeping operations, a new Lake Sinai virus, and a sequence variant of acute bee paralysis virus. In addition, we re-sequenced the genomes of 16 previously characterized bee and/or <i>Varroa destructor</i> mite infecting viruses and two previously described, but not well-characterized, partitivirus-like sequences (i.e., Apis mellifera associated partiti-like virus 1 and Hubeipartiti-like virus 34). Virus abundance was greater in libraries representing colonies that died during the monitoring period.