Fig. 8: In silico demonstration of novel, sequence-divergent virus detection using the mNGS assay. | Nature Communications

Fig. 8: In silico demonstration of novel, sequence-divergent virus detection using the mNGS assay.

From: Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery

Fig. 8

A Representative viral reference genomes corresponding to outbreak viruses of clinical and public health significance with pandemic potential are retrieved from the NCBI GenBank database, partitioned into non-overlapping segments, and then randomly sampled and spiked in silico into a negative nasal swab matrix sequencing library. A higher-level set of taxonomic identifiers (species, genus, and/or family) corresponding to these viruses is removed from the SURPI+ reference dataset and the simulated sequencing file is analyzed using both the original and “restricted reference” databases. B Viruses can be detected using the modified SURPI+ pipeline despite lacking a taxonomic reference at levels down to 10–100 reads per million (RPM). Abbreviations: EEEV Eastern equine encephalitis virus, ERCC External RNA Controls Consortium, FDA-ARGOS FDA dAtabase for Reference Grade micrObial Sequences, HFV hemorrhagic fever virus, HIV human immunodeficiency virus, JCPyV JC polyomavirus, PC positive control, PyV polyomavirus, TSPyV trichodysplasia spinulosa polyomavirus, SURPI+ sequence-based ultrarapid pathogen identification, VEEV Venezuelan equine encephalitis virus, WEEV Western equine encephalitis virus.

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