Adaptation of custom capture sequencing panels to the Oxford Nanopore Minion platform

NGS remains underutilized in clinical microbiology applications despite providing broad pathogen spectrum detection superior to other molecular methods. This is primarily because of lower sensitivity of metagenomic NGS (mNGS) compared to PCR, lengthy turn-around times, cost, and complexity of data analysis. Capture sequencing is a technique that can mitigate the limitations of NGS. Using probes that are engineered to selectively bind and pull down desired nucleic acids, capture sequencing enriches for targets of interest and can result in up to a 10,000-fold increase in sensitivity compared to mNGS. Here, we describe the application of capture sequencing on ONT portable sequencer, the MinION MK1C. We examined VirCapSeq-VERT and TBDCapSeq, two distinct capture sequencing assays that target vertebrate viruses, and tick-borne pathogens, respectively. Both assays were originally established on the Illumina platform. In direct comparison tests using contrived and clinical samples, we achieved equivalent sensitivity on the MinION MK1C and Illumina NextSeq for both assays. These findings suggest the potential of the MinION platform in field applications during outbreak responses and for accelerated clinical diagnostics.