Enrichment and Sequencing of Viral DNA

For the enrichment of viral fragments contained in the synthesized libraries, several libraries were pooled to perform the capture step, as described before^{31 (link)}. Briefly, the pooled libraries were mixed with the virus-specific probes in the presence of human Cot-1 DNA (Invitrogen) and xGen universal blocking oligos (IDT) for the hybridization step. A series of wash steps were performed using DNA xGen lockdown reagents (IDT), following the manufacturer’s recommendations. The quality of the enriched DNA libraries was evaluated by electrophoresis with a TapeStation 2200 system (Agilent Technologies) and quantified by real time PCR with the GenNext NGS library quantification kit (Toyobo). Finally, the multiplexed libraries were subjected to cluster generation using a MiSeq Reagent Kit v3 (150 cycles) or NextSeq 500 Kit (75 cycles) in MiSeq or NextSeq desktop sequencing systems (Illumina), respectively.