negative control
Samples were homogenised and filtered through a 0.45 m filter to concentrate virus-like particles (VLPs). Nucleic acids not protected in VLPs were degraded by DNase and RNase incubation at 37C for 1.5 h. Total RNA and DNA were then extracted using a QIAamp Viral RNA Mini Kit (Qiagen).  Reverse transcription was performed using SuperScript IV VILO kit (Invitrogen), cDNAs were purified by a QIAquick PCR Purification Kit (Qiagen)  and complementary strands synthesised by Klenow DNA polymerase I (Promega). Double-stranded DNA was amplified by random PCR amplification  (Q5 Hot Start High-Fidelity kit, New England Biolabs). Samples were barcoded during reverse transcription and PCR steps using homemade 26-nt Dodeca Linkers and PCR  multiplex identifier primers. PCR products were purified using a NucleoSpin gel and PCR clean-up kit (Macherey Nagel). dsDNAs were quantified using a Qubit 1X dsDNA HS assay kit. Libraries were prepared using a NEB NEXT Ultra II DNA Library prep kit, and sequenced on a NovaSeq6000 in 2x150bp paired-end mode (Oxford Genomics, UK).