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Abstract Metagenomic sequencing is a powerful technique that enables detection of the full spectrum of pathogens present in any specimen in a single test. Hence, metagenomics is increasingly being applied for detection of viruses in clinical cases with suspected infections of unknown etiology and a large number of relevant potential causes. This is typically the case in patients presenting with encephalitis, in particular when immunity is impaired by underlying disorders. In this study, viral metagenomics has been applied to a cohort of hematological patients with encephalitis of unknown origin. Since viral loads in cerebrospinal fluid of patients with encephalitis are generally low, the technical performance of a metagenomic sequencing protocol enriched by capture probes targeting all known vertebrate viral sequences was studied. Subsequently, the optimized viral metagenomics protocol was applied to a cohort of hematological patients with encephalitis of unknown origin. Viral enrichment by capture probes increased the viral sequence read count of metagenomics on cerebrospinal fluid samples 100 – 10.000 fold, compared to unenriched metagenomic sequencing. In five out of 41 (12%) hematological patients with encephalitis, a virus was detected by viral metagenomics which had not been detected by current routine diagnostics. BK polyomavirus, hepatitis E virus, human herpes virus-6 and Epstein Barr virus were identified by this unbiased metagenomic approach. This study demonstrated that hematological patients with encephalitis of unknown origin may benefit from early viral metagenomics testing as a single step approach. Highlights A metagenomics protocol employing virus capture probes was validated and retrospectively applied to 41 hematological adult and pediatric patients presenting with encephalitis of unknown aetiology Viral enrichment by capture probes increased sensitivity of viral metagenomics on cerebrospinal fluid samples 100 – 10.000 fold, compared to unenriched metagenomic sequencing In 12% of hematological patients with encephalitis of unknown origin, a virus was detected by viral metagenomics, which was not found by routine diagnostics Viral metagenomics represents a valuable addition to the diagnostics repertoire for hematological patients with suspected CNS infection
Carbo et al. (Sat,) studied this question.