Nuno Taveira, group leader and Inês Bártolo, researcher of the HIV Evolution, Epidemiology and Prevention Lab at iMed.ULisboa are authors of the study Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance, just published in Nature Microbiology.
Metagenomic 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. In this paper, the authors developed a spiked primer enrichment method (MSSPE method) for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. A median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone was obtained. 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. 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.
The manuscript can be read, here.