Abstract
Metagenomic next-generation sequencing (mNGS) can capture the full spectrum of viral pathogens in a specimen and has the potential to become an all-in-one solution for virus diagnostics. To date, clinical application is still in an early phase and limitations remain. Here, we evaluated the impact of viral mNGS for cases analyzed over two years in a tertiary diagnostics unit. High throughput mNGS was performed upon request by the treating clinician in cases where the etiology of infection remained unknown or the initial differential diagnosis was very broad. The results were compared to conventional routine testing regarding outcome and workload. In total, 163 specimens from 105 patients were sequenced. The main sample types were cerebrospinal fluid (34%), blood (33%) and throat swabs (10%). In the majority of the cases, viral encephalitis/meningitis or respiratory infection was suspected. In parallel, conventional virus diagnostic tests were performed (mean 18.5 individually probed targets/patients). mNGS detected viruses in 34 cases (32%). While often confirmatory, in multiple cases, the identified viruses were not included in the selected routine diagnostic tests. Two years of mNGS in a tertiary diagnostics unit demonstrated the advantages of a single, untargeted approach for comprehensive, rapid and efficient virus diagnostics, confirming the utility of mNGS in complementing current routine tests.
Highlights
Viruses are one of the major causes of human infectious diseases
In 2017, we introduced virus sequence-independent metagenomic high-throughput sequencing at our tertiary diagnostic unit and established protocols for sample preparation, sequencing and bioinformatics analysis [26]
We systematically evaluated the impact of Metagenomic next-generation sequencing (mNGS) on diagnosis, comparing outcome and workload to results obtained by conventional routine testing in these cases
Summary
The identification of the causative pathogen remains challenging in several disease settings [1–4] Many clinical syndromes, such as viral meningitis/encephalitis, respiratory syndromes or febrile illness often call for a broad differential diagnosis. This results in extensive diagnostic testing most commonly in an iterative manner starting with the most likely pathogens. In 2017, we introduced virus sequence-independent metagenomic high-throughput sequencing at our tertiary diagnostic unit and established protocols for sample preparation, sequencing and bioinformatics analysis [26] This analysis workflow has proven highly successful enabling us to detect disease causing viral pathogens in complex clinical cases [27–29]. We systematically evaluated the impact of mNGS on diagnosis, comparing outcome and workload to results obtained by conventional routine testing in these cases
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