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

Area of Science:

• Virology
• Genomics
• Biosafety

Background:

• Genomic research on Risk Group 4 (RG4) viruses is challenging due to strict biosafety level 4 (BSL-4) requirements.
• Inactivating RG4 viruses before BSL-4 containment removal often degrades nucleic acid, hindering genomic studies.

Purpose of the Study:

• To develop and validate optimized workflows for safe genomic analysis of RG4 viruses within BSL-4 containment.
• To maintain nucleic acid integrity during inactivation and extraction for next-generation sequencing (NGS) applications.

Main Methods:

• Systematic assessment of inactivation, homogenization, and RNA extraction methods for bulk RNA sequencing.
• Adaptation of single-cell RNA sequencing (scRNA-seq) with integrated inactivation steps.
• Optimization of viral genome enrichment strategies for high-depth sequencing.

Main Results:

• Established robust bulk RNA sequencing workflows compatible with BSL-4 containment and diverse sample types.
• Demonstrated successful scRNA-seq on Lassa virus-exposed cells without compromising data quality.
• Optimized viral genome enrichment for high-depth sequencing of multiple RG4 viruses.

Conclusions:

• Validated workflows enable safe and reproducible genomic analyses of RG4 pathogens under BSL-4 conditions.
• These methods significantly expand the experimental toolkit for high-resolution genomic research on dangerous viruses.
• The developed protocols preserve nucleic acid integrity, facilitating advanced sequencing applications in high-containment settings.