HIV-PULSE: A long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization
A PCR reaction with bulk DNA containing multiple HIV-1 templates is pre-amplified using outer HIV-1 primers for a limited number of cycles to improve sensitivity. Next, pre-amplified material is tagged with a dual barcode consisting of a unique molecular identifier (UMI) attached to both ends using an HIV-1 specific inner primer. To generate enough material for long-read library preparation, the tagged material is amplified with synthetic primers in several PCR rounds followed by clean up to prevent length bias.