Integrated Antigenic and Nucleic Acid Detection in Single Virions and Extracellular Vesicles with Viral Content

Virion‐mediated outbreaks are imminent and despite rapid responses, continue to cause adverse symptoms and death. Therefore, tunable, sensitive, high‐throughput assays are needed to help diagnose future virion‐mediated outbreaks. Herein, it is developed a tunable in situ assay to selectively enrich virions and extracellular vesicles (EVs) and simultaneously detect antigens and nucleic acids at a single‐particle resolution. The Biochip Antigen and RNA Assay (BARA) enhanced sensitivities compared to quantitative reverse‐transcription polymerase chain reaction (qRT‐PCR), enabling the detection of virions in asymptomatic patients, genetic mutations in single virions, and enabling the continued long‐term expression of viral RNA in the EV‐enriched subpopulation in the plasma of patients with post‐acute sequelae of the coronavirus disease of 2019 (COVID‐19). BARA revealed highly accurate diagnoses of COVID‐19 by simultaneously detecting the spike glycoprotein and nucleocapsid‐encoding RNA in saliva and nasopharyngeal swab samples. Altogether, the single‐particle detection of antigens and viral RNA provides a tunable framework for the diagnosis, monitoring, and mutation screening of current and future outbreaks. The Biochip Antigen and RNA Assay (BARA) enables simultaneous antigenic and nucleic acid detection of virions and EVs with viral content at a single‐particle resolution. BARA provides unprecedented perspectives on viral diseases, including enhanced sensitivity without amplification, colocalization of biomolecules on intact virions and EVs, accurate diagnoses, and assay adaptability.