Landscape-scale virome analysis uncovers endemic and emerging honey bee viruses in the Silk-Road hub of Uzbekistan

Honey bee health is increasingly threatened worldwide by a complex and evolving viral landscape; however, this aspect in Central Asia remains understudied despite the region being strategically positioned along historic and modern trade routes. In 2024, we conducted a nationwide virome survey of Apis mellifera across 32 cities in 11 regions of Uzbekistan, combining the metagenomic data of 14 pooled RNA-seq libraries with RT-PCR validation and phylogenetic analyses. High-quality sequencing yielded an average of approximately 60 million reads per pool. We recovered 30 viral species from 162 genomic sequences (131 complete sequences), including 11 honey bee-associated and 19 plant-infecting viruses. All samples harbored deformed wing virus type A (DWV-A), and co-infection with DWV-B predominated. Our findings provided the first full-length DWV-B genomes from Central Asia, revealing that it had > 97 % identity to European strains. New variants of the Sacbrood virus (partial sequence, approximately 4.7 kb) and Lake Sinai virus UZB were also detected. The chronic bee paralysis virus was sequenced in full for the first time in Uzbekistan, and varroa orthomyxovirus-1 exhibited segment-specific divergence. Additionally, we identified two novel plant viruses: Gulistan nepovirus 1 and Arpa carmo-like virus 1. Phylogenetic patterns of the identified viruses indicate that Uzbekistan serves as a genetic corridor connecting European and Asian virus populations. These findings fill critical geographical gaps, underscore the need for transboundary surveillance, and provide a genomic baseline for future diagnostics, epidemiology, and control strategies aimed at safeguarding pollinator and ecosystem health.