Evaluation of a custom designed hybridisation assay for whole genome sequencing of human adenoviruses direct from clinical samples

Abstract

Background: Human Adenoviruses are a common cause of disease and can cause significant morbidity and mortality in immunocompromised patients. Nosocomial transmission events can occur with whole genome sequencing playing a crucial role. This study evaluates the performance of a custom designed SureSelect^XT target enrichment assay based on 14 adenovirus genomes for sequencing direct from clinical samples.

Methods: Modifications were made to the SureSelect^XT low input protocol to enhance performance for viral targets. Consensus sequences were generated using an in-house designed three stage bioinformatics pipeline. We assessed, percentage of on target reads, average depth of coverage and percentage genome coverage to determine assay performance across a range of sample matrices.

Results: Whole genome sequences were successfully generated for 91.6 % of samples assessed. Adenovirus DNA concentration was a good indicator of enrichment success. Highly specific enrichment was observed with only 6 % of samples showing < 50 % on target reads. Respiratory and faecal samples performed well where bloods showed higher levels of non-specific enrichment likely confounded by low adenovirus DNA concentrations. Protocol performance did not appear impacted by Adenovirus type or species.

Conclusion: Overall performance of this modified SureSelect^XT protocol appears in line with previously published works although there are some confounding factors requiring further investigation. The use of a small RNA bait set has the potential to reduce associated costs which can be prohibitive.

Keywords: Adenovirus; Hybrid capture, Agilent, SureSelect; Targeted enrichment; Whole genome sequencing.