Enhanced virome sequencing using targeted sequence capture.

Area of Science:

• Virology
• Genomics
• Bioinformatics

Background:

• Metagenomic shotgun sequencing (MSS) is crucial for viral population characterization but often lacks sensitivity and sufficient data.
• Targeted enrichment methods are needed to overcome limitations of standard MSS for comprehensive viral analysis.

Purpose of the Study:

• To develop and evaluate ViroCap, a targeted sequence capture panel, for enhancing viral detection and genomic representation in vertebrate-infecting viruses.
• To compare the efficacy of ViroCap-enriched MSS against standard MSS for viral discovery.

Main Methods:

• ViroCap was designed using a computational approach to condense viral reference sequences for targeted capture of DNA and RNA viruses from 34 families.
• The performance of ViroCap was assessed by analyzing diagnostic and pediatric fever study samples using both standard MSS and ViroCap-enriched MSS.
• Anellovirus detection was performed to evaluate ViroCap's ability to identify sequences with significant variation from reference probes.

Main Results:

• ViroCap dramatically enhanced viral genome representation, with median fold-increases in viral reads of 674 and 296 in the analyzed sample sets.
• Median breadth of coverage significantly increased post-capture, from 2.1% to 83.2% and 2.0% to 75.6%.
• ViroCap successfully detected diverse anellovirus sequences with up to 58% variation from reference probes.

Conclusions:

• ViroCap substantially improves the sensitivity and scope of metagenomic shotgun sequencing for detecting a wide range of viruses.
• The ViroCap panel offers significant utility for both viral research and clinical diagnostic applications, enabling more comprehensive viral profiling.