Paired aptamer capture and FISH detection of individual virions enables cell-free determination of infectious titer

Early detection of viruses can prevent the uncontrolled spread of viral infections. Determination of viral infectivity is also critical for determining the dosage of gene therapies, including vector-based vaccines, CAR T-cell therapies, and CRISPR therapeutics. In both cases, for viral pathogens and viral vector delivery vehicles, fast and accurate measurement of infectious titer is desirable. The most common methods for virus detection are antigen-based (rapid but not sensitive) and reverse transcription polymerase chain reaction (RT-PCR)-based (sensitive but not rapid). Current viral titer methods heavily rely on cultured cells, which introduces variability within labs and between labs. Thus, it is highly desirable to directly determine the infectious titer without using cells. Here, we report the development of a direct, fast, and sensitive assay for virus detection (dubbed rapid-aptamer FISH or raptamer FISH) and cell-free determination of infectious titers. Importantly, we demonstrate that the virions captured are "infectious," thus serving as a more consistent proxy of infectious titer. This assay is unique because it first captures viruses bearing an intact coat protein using an aptamer, then detects genomes directly in individual virions using fluorescence in situ hybridization (FISH)- thus, it is selective for infectious particles (i.e., positive for coat protein and positive for genome).