Genomics in containment: BSL-4-compatible workflows enable high-resolution genomic and transcriptomic analyses of Risk Group 4 viruses

Genomic research on high-consequence Risk Group 4 (RG4) viruses is significantly hindered by the stringent biosafety level 4 (BSL-4) containment requirements, because virus inactivation prior to removal from containment often compromises nucleic acid integrity. As a focused solution to retain nucleic acid integrity as well as safety compliance, we developed and validated a comprehensive suite of optimized workflows compatible with BSL-4 containment and next-generation sequencing applications. We systematically assessed inactivation, homogenization, and RNA extraction methods to establish robust bulk RNA sequencing workflows for diverse sample types. We also adapted state-of-the-art single-cell RNA sequencing (scRNA-seq) by integrating inactivation steps without compromising data quality. To demonstrate feasibility, we conducted scRNA-seq analysis on cells exposed to Lassa virus. Additionally, we optimized viral genome enrichment strategies for high-depth sequencing of multiple RG4 viruses. These validated workflows enable safe, reproducible, and high-resolution genomic analyses of RG4 pathogens, significantly expanding the experimental toolkit for BSL-4 research.