Libraries were prepared by essentially following the standard KAPA protocol but including viral sequence capture, following mainly the SeqCap RNA enrichment system protocol (Roche/NimbleGen). Briefly, total NA extract was reverse transcribed using SuperScript III (Thermo, Fisher) with random hexamers. The cDNA was RNase H treated prior to second-strand synthesis with Klenow fragment (New England Biolabs). The resulting double-stranded cDNA/DNA mix was sheared to an average fragment size of 200 bp using the manufacturer’s standard settings (Covaris E210 focused ultrasonicator). Sheared product was purified (AxyPrep), and libraries were constructed using KAPA library preparation kits (KAPA) with Roche/NimbleGen adapter kits. The quality and quantity of libraries were checked using a Bioanalyzer (Agilent). The libraries were then mixed with a SeqCap HE universal oligonucleotide, SeqCap HE index oligonucleotides, and COT DNA and vacuum evaporated at 60°C for approximately 40 min. Dried samples were mixed with 2× hybridization buffer and hybridization component A (Roche/NimbleGen) prior to denaturation at 95°C for 10 min. The VirCap probe library (4.5 μl) was added and hybridized at 47°C for 12 h in a standard PCR thermocycler. SeqCap Pure capture beads (Roche/NimbleGen) were washed twice, mixed with the hybridization mix, and kept at 47°C for 45 min with vortexing for 10 s every 10 to 15 min. The streptavidin capture beads complexed with biotinylated VirCapSeq-VERT probes were trapped (DynaMag-2 magnet; Thermo, Fisher) and washed once at 47°C and then twice more at room temperature with wash buffers of increasing stringency. Finally, beads were suspended in 50 µl water and directly subjected to posthybridization PCR (SeqCap EZ accessory kit V2; Roche/NimbleGen). The PCR products were purified (Agencourt Ampure DNA purification beads; Beckman Coulter, Brea, CA, USA) and quantitated by Bioanalyzer (Agilent) for Illumina sequencing.