Next generation sequencing of honey bee colonies from four California beekeeping operations

Honey bees were sampled from individual colonies from four California based beekeeping operations, with sampling dates between August 2022 - January 2023. Ten bees from each colony were randomly selected and homogenized to generate colony level lysates. Colony-level lysates were pooled based on shared characteristics (i.e., beekeeping operation, sampling date, population loss, and Varroa destructor mite infestation pressure). Pooled lysates were treated with nucleases to degrade host nucleic acid, enriching for encapsidated viral nucleic acids. RNA was extracted from these virus enriched samples. Libraries were prepared for sequencing using a Watchmaker RNA Prep Kit (Illumina) without PolyA selection or rRNA depletion. Libraries were sequenced on an Illumina Novaseq X Plus 25B, generating 150bp paired end reads. An average of 8.2 million reads were generated per library. Sequencing libraries represented colonies with similar characteristics (i.e., from same beekeeping operation, sampled at the same time, experienced the same population dynamics, and mite pressure).