Profiling of honey bee viruses in Kenyan honey bee colonies

Abstract

Honey bee population worldwide is dwindling due to a number of interrelated factors among them pathogens such as viruses, bacteria, fungi and metazoan parasites. These factors negatively affect agricultural production as well as the apiculture industry which is dependent on a seasonal abundance of honey bees year-round. As a result, food security and livelihood is compromised due to loss of pollinators. Majority of viruses infecting honey bees are positive-sense single-stranded RNA viruses of the order Picornavirales. The economically important viruses of bees in this order belong to family Dicistroviridae and Iflaviridae. Paenibacillus larvae and Melisococcus plutonius are bacteria known to cause bee brood diseases. This study
aimed at identifying the viruses circulating in Kenyan honey bee colonies using next generation sequencing. Ribonucleic acid (RNA) was extracted from sixteen libraries and was used in cDNA synthesis using superscript II. The cDNA converted to dsDNA using Klenow reaction and used in amplification. 454 pyro sequencing was performed on genome sequencer FLX system. The resultant single reads were analyzed using CLC Genomic workbench. The reads were mapped on the full genomes of the identified viruses and then de novo assembled. The resultant contigs were interrogated using basic alignment search tool (BLAST) on national center for biotechnology information (NCBI) database. The contigs were exported
to MEGA6 and used in phylogenetic analysis. The viruses identified belonged to family Iflaviridae and included deformed wing virus, Kakugo virus and Varroa destructor virus-1. Melissococcus plutonius and Enterococcus faecalis were also detected. Of the sixteen libraries sequenced, two libraries; Busia_adult and
Siaya_brood reported the incidences of iflaviruses while five libraries had reads matching with M. plutonius and E. faecalis. There is need for a strategy in place for the management of bee diseases to enhance bee health and quality of hive products.

Key words: Bee viruses, Paenibacillus larvae, Melissococcus plutonius, Iflavirus, Next generation sequencing