  Genetic analysis methods are foundational to advancing personalized and
preventative medicine, accelerating disease diagnostics, and monitoring the
health of organisms and ecosystems. Current nucleic acid technologies such as
polymerase chain reaction (PCR), next-generation sequencing (NGS), and DNA
microarrays rely on fluorescence and absorbance, necessitating sample
amplification or replication and leading to increased processing time and cost.
Here, we introduce a label-free genetic screening platform based on high
quality (high-Q) factor silicon nanoantennas functionalized with monolayers of
nucleic acid fragments. Each nanoantenna exhibits substantial electromagnetic
field enhancements with sufficiently localized fields to ensure isolation from
neighboring resonators, enabling dense biosensor integration. We quantitatively
detect complementary target sequences using DNA hybridization simultaneously
for arrays of sensing elements patterned at densities of 160,000 pixels per
cm$^2$. In physiological buffer, our nanoantennas exhibit average resonant
quality factors of 2,200, allowing detection of two gene fragments, SARS-CoV-2
envelope (E) and open reading frame 1b (ORF1b), down to femtomolar
concentrations. We also demonstrate high specificity sensing in clinical
nasopharyngeal eluates within 5 minutes of sample introduction. Combined with
advances in biomarker isolation from complex samples (e.g., mucus, blood,
wastewater), our work provides a foundation for rapid, compact,
amplification-free and high throughput multiplexed genetic screening assays
spanning medical diagnostics to environmental monitoring.
