Molecular characterization of viruses found in honeybee (Apis mellifera) colonies infested with Varroa destructor and Nosema cerana in Egypt.

Honey bees (Apis mellifera) have a vital role as pollinators of various crops in the global food supply. Honeybee colonies in Egypt have recently experienced an unexplained rise in annual loss due to a phenomenon known as Colony Collapse Disorder (CCD). In the current study, honey bees were collected from 14 sites from eight governorates in Egypt. The genetic diversity among the collected honey bee populations was investigated using the mitochondrial DNA cytochrome oxidase subunit I (COI). The amplified COI regions were sequenced, analyzed and aligned with other GenBank entries. The nucleotide variability of the CO1 gene was estimated. Multiple viral, varroa mites as well as Nosema ceranae infections were tested in honey bee populations using conventional and RT-qPCR. Based on sequence analysis of the COI, six clearly separated mitotypes were characterized for the first time in these sites in Egypt. Sequence analyses showed that most mitotypes belonged to the A lineage and are very close to the Egyptian native bees, A. m. lamarckii found in the gene databank (NCBI) with 98% similarity. Low genetic diversity between the collected samples was observed. Our results elucidated the detection of Nosema cerana; deformed wing virus (DWV), kakugo virus (KV), black queen/cell virus (BQCV), Israel acute paralysis virus (IAPV), varroa destructor virus-1 (VDV-1) and VDV-1/DWV virus in all regions under investigation in addition to varroa mites. These findings highlighted the importance to maintain proper quarantine measures as well as identify the spectrum of exogenous infectious agents in healthy hives over time which would help in developing more effective control and treatment programs against honey bee viruses and pathogens to facilitate efficient breeding programs and establish a more booming beekeeping industry.