South Korea experienced a significant decline in honey bee populations starting in 2021, which continued for two years until the winter of 2022. To investigate the potential causes of this decline, we conducted a virome analysis, considering viruses as possible culprits. Samples were collected during two periods: April-May 2022 and May-June 2023. From libraries contsructed from their total RNA, we secured a total of 25 raw FASTQ files by high-throughput sequencing. In the honey bees collected in 2022, we identified eight previously unreported honey bee viruses including Lake Sinai viruses, one novel honey bee-related virus, and one novel plant-related virus. In the subsequent sampling in 2023, we found that most of the viruses identified in 2022 were still present. Additionally, the novel honey bee virus reported in 2022 was also found in the 2023 collections, along with three more honey bee-related novel viruses. Notably, numerous plant viruses were detected in honey bees collected during the flowering season. This analysis suggests that the viruses observed in South Korean honey bees are likely distributed nationwide. These findings provide fundamental data for future research on honey bee viruses in South Korea.

Over the course of two winters, the significant decline in honey bee populations in Korea has emerged as a major social issue. This phenomenon is expected as attributed to factors such as the failure of pest control due to the pesticide resistance of the Varroa mite. This mite can transmit some viruses that infect honey bees, and these viruses are among the primary causes of the globally occurring colony collapse disorder. Traditional diagnostic methods like (RT-)PCR and ELISA are not ideal for identifying pathogens that are newly emerging or have undergone mutations. To detect any novel or mutated viruses beyond those that have been primarily diagnosed in Korea, we introduced virome analysis technology in the field of honey bees. Employing this method with high-throughput sequencing techniques, we were able to identify all existing viruses within individual or group samples. We discovered that the Lake Sinai virus, which has been reported worldwide but not in Korea, has already significantly spread within the country. Additionally, we were able to confirm the prevalence of viruses previously reported in Korea, such as the recently dominant Black Queen Cell Virus. Through this virome analysis, we can provide foundational data for determining the direction and countermeasures for virus diagnosis.