Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples

• Published in: Journal of clinical microbiology Vol. 62; no. 6; p. e0034524
• Main Authors: Mourik, Kees, Sidorov, Igor, Carbo, Ellen C, van der Meer, David, Boot, Arnoud, Kroes, Aloysius C M, Claas, Eric C J, Boers, Stefan A, de Vries, Jutte J C
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 12.06.2024
• Subjects: Humans; Innovative Diagnostic Methods; Limit of Detection; Metagenomics - methods; Metagenomics - standards; Molecular Diagnostic Techniques - methods; Molecular Diagnostic Techniques - standards; Nucleic Acid Hybridization - methods; Reference Standards; Sensitivity and Specificity; Virology; Virome; Virus Diseases - diagnosis; Virus Diseases - virology; Viruses - classification; Viruses - genetics; Viruses - isolation & purification; capture probes; targeted metagenomics; viral metagenomics; viral diagnostics
• ISSN: 0095-1137; 1098-660X; 1098-660X
• DOI: 10.1128/jcm.00345-24

Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares the analytical performance of two targeted metagenomic virus capture probe-based methods: (i) SeqCap EZ HyperCap by Roche (ViroCap) and (ii) Twist Comprehensive Viral Research Panel workflow, for diagnostic use. Sensitivity, specificity, and limit of detection were analyzed using 25 synthetic viral sequences spiked in increasing proportions of human background DNA, eight clinical samples, and American Type Culture Collection (ATCC) Virome Virus Mix. Sensitivity and specificity were 95% and higher for both methods using the synthetic and reference controls as gold standard. Combining thresholds for viral sequence read counts and genome coverage [respectively 500 reads per million (RPM) and 10% coverage] resulted in optimal prediction of true positive results. Limits of detection were approximately 50-500 copies/mL for both methods as determined by ddPCR. Increasing proportions of spike-in cell-free human background sequences up to 99.999% (50 ng/mL) did not negatively affect viral detection, suggesting effective capture of viral sequences. These data show analytical performances in ranges applicable to clinical samples, for both probe hybridization metagenomic approaches. This study supports further steps toward more widespread use of viral metagenomics for pathogen detection, in clinical and surveillance settings using low biomass samples. Viral metagenomics has been gradually applied for broad-spectrum pathogen detection of infectious diseases, surveillance of emerging diseases, and pathogen discovery. Viral enrichment by probe hybridization methods has been reported to significantly increase the sensitivity of viral metagenomics. During the past years, a specific hybridization panel distributed by Roche has been adopted in a broad range of different clinical and zoonotic settings. Recently, Twist Bioscience has released a new hybridization panel targeting human and animal viruses. This is the first report comparing the performance of viral metagenomic hybridization panels.