Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance
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AbstractMetagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use.
DescriptionAuthor Correction: In the version of this Article originally published, the sentence beginning “We also used MPSSE to enrich...” should have stated that the samples were from a patient who developed a fatal viral encephalitis following a ‘mosquito bite’ rather than a ‘tick bite’. The sentence has now been corrected to read: “We also used MSSPE to enrich for Jamestown Canyon virus (JCV) in post-mortem brain tissue samples from a patient who developed a fatal viral encephalitis following a mosquito bite”. Correction DOI 10.1038/s41564-020-0671-7.
SponsorsThis work was also funded in part by Abbott Laboratories, NIH grant no. R33-AI129455 from the NIAID, NIH grant no. R01-HL105704 from the National Heart, Lung, and Blood Institute, the California Initiative to Advance Precision Medicine, the Charles and Helen Schwab Foundation, the Steven and Alexandra Cohen Foundation, United States Department of Defense award W81XWH-17-1-0681, the Wellcome Trust and Royal Society/Sir Henry Dale Fellowship grant no. 204311/Z/16/Z, the Global Challenges Research Fund grant no. 005073, the Oxford John Fell Research Fund grant no. 005166 and Africa Oxford grant no. AfiOx-48.
Identifier to cite or link to this itemhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85077844387&doi=10.1038%2fs41564-019-0637-9&partnerID=40&md5=b7720616f8763a15e57a9c6968139a3e; http://hdl.handle.net/10713/11688