Integrated antigenic and nucleic acid detection in single virions and virion-infected host-derived extracellular vesicles

Virion-mediated outbreaks are imminent and despite rapid responses, they continue to cause adverse symptoms and death. Therefore, tunable, sensitive, high-throughput assays are needed to control future virion-mediated outbreaks. Herein, we developed a tunable in situ assay to selectively sort virions and infected host-derived extracellular vesicles (IHD-EVs) and simultaneously detect antigens and nucleic acids at a single-particle resolution. The Biochip Antigen and RNA Assay (BARA) enhanced sensitivities, enabling the detection of virions in asymptomatic patients, genetic mutations in single virions, and the continued long-term expression of virion-RNA in the IHD-EVs of post-acute sequelae of COVID-19 patients. The BARA revealed highly accurate diagnoses by simultaneously detecting the spike glycoprotein and nucleocapsid-encoding RNA on single SARS-CoV-2 virions in saliva and nasopharyngeal swab samples. Altogether, the single-particle detection of antigens and virion-RNA provides a tunable framework for the diagnosis, monitoring, and mutation screening of current and future outbreaks.