Target-enrichment of porcine nasal swab: Enrichment XTHS2
Utilizing field samples, RNA was extracted (1), and cDNA synthesis was performed (2). Then, library preparation was executed (3) followed by the hybridization process in which custom-designed biotinylated 120-mer probes (4) were used to capture the targeted viruses with streptavidin-coated magnetic beads (5). Captured fragments were amplified and submitted for sequencing using the minION platform from Oxford Nanopore Technologies (6). Resulting TELSVirus reads were trimmed for adapters and deduplicated (7). Subsequently, reads that aligned to the host genome (i.e., Sus scrofa) were removed, referred to as off-target reads (8). The remaining reads were then aligned to the viral reference genomes, termed on-target reads (9).