Illumina MiSeq paired end sequencing
RNA was transcribed into cDNA using random hexamers (Thermo Fisher) and SuperScript IV (Thermo Fisher) and dsDNA was generated using Klenow (NEB). A specific capture for all vertebrate viruses was performed using VirCapSeq capture probes. The capture was performed according to the manufacturerï¿½s instruction (Roche) and the hybridization reaction was incubated for 72 hours.