ddPCR was performed using a previously described duplex assay25 (link) with the primers and probes given in Supplementary Table S3 . VLPs were lysed by heating to 95°C for 5 min in a thermocycler before being added to ddPCRs. ddPCRs (20 μL) used ddPCR™ Multiplex Supermix (Bio Rad) with final primer and probe concentrations of 900 and 250 nM and a sample volume of 2 μL. Droplets were then generated using a QX200™ Droplet Generator (Bio Rad) and transferred to a PCR plate and sealed, all according to the manufacturer's instructions.
The reaction mixture was then thermocycled (95°C for 10:00, 40 cycles of 94°C for 0:30, and 60°C for 1:00, and a final enzyme inactivation step of 98°C for 10:00) on a BioRad C1000 touch PCR machine. Finally, droplets were read using the QX200 Droplet Reader (Bio Rad). Data were then analyzed using a Python implementation (https://github.com/mcrone/plotlydefinerain ) of an online tool called Defining The Rain (https://definetherain.org.uk/ ) with added support for two color channels.
The reaction mixture was then thermocycled (95°C for 10:00, 40 cycles of 94°C for 0:30, and 60°C for 1:00, and a final enzyme inactivation step of 98°C for 10:00) on a BioRad C1000 touch PCR machine. Finally, droplets were read using the QX200 Droplet Reader (Bio Rad). Data were then analyzed using a Python implementation (
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