Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device.

Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.

A nano-magnetic size selective cfDNA extraction platform for liquid biopsy with enhanced precision.

As an emerging biomarker, cell-free DNA (cfDNA) carries crucial genetic information for the diagnosis of hereditary disease and cancer. However, test accuracy was severely compromised by the low abundance of cell-free DNA in peripheral blood, frequently diluted by genomic DNA released from white blood cells, resulting in sample rejection, test inaccuracy, and restricted clinical utility. Herein we report a novel strategy for the efficient recovery of cfDNA with significant removal of genomic DNA contamination during the cfDNA extraction process, based on a nano-magnetic size selective cfDNA extraction platform. With this platform, over 90% cfDNA recovery rate was achieved with minimal genomic DNA contamination. For non-invasive prenatal testing, an increase of fetal fraction from 10.10% to 29.94% medially was observed in 11 maternal plasma samples, with two false-negative samples identified by the proposed workflow. Enrichment of cfDNA in plasma sample of cancer patient demonstrated âˆ¼ 100% increase of circulating tumor DNA (ctDNA) percentage by panel sequencing of specific mutation sites. The approach is simple, automatable and cost-efficient, can improve liquid biopsy precision and reduce sequencing depth through significant enrichment of target abundance. The nano-magnetic platform demonstrated its potential application in liquid biopsy, since it exhibited numerous advantages in avoiding false negative results, reducing sequencing cost, improving data quality, and rescuing contaminated samples.