A novel High-Throughput Ligase-Independent Mapping method to detect Viral Integration Sites

Authors

Kabi, M., Anreiter, I., Filion, G. J.

Abstract

Integrated DNA elements are central to virology, functional genomics, and gene therapy, but current insertion-site mapping methods often rely on restriction digestion, ligation, or complex sequencing workflows that introduce bias and limit recovery. Here, we present Terminal Mapping, a high-throughput method that identifies host-insert junctions without restriction enzymes or DNA ligation. The workflow combines linear amplification from a known terminal sequence, enrichment of single-stranded products, terminal transferase-mediated poly-A tailing, and PCR amplification for Illumina or Oxford Nanopore sequencing. Applied to Jurkat T cells transduced with HIV-1- and SIVmac251-derived vectors, Terminal Mapping recovered more HIV-1 insertion sites than inverse PCR, reproduced known integration biases, and showed improved robustness with long-read sequencing. It revealed shared but quantitatively distinct HIV-1 and SIVmac251 hotspots, as well as substantial differences between Jurkat cell sources. Comparison of 5' and 3' LTR-derived reads also provided an internal control for unintegrated viral DNA. Terminal Mapping therefore offers a rapid and flexible platform for profiling integrated genetic elements across vectors and cellular contexts.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 16 Jun 2026.

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