title: Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip.
abstract: Viral infections are a major cause of human disease, but many require molecular assays for conclusive diagnosis. Current assays typically rely on RT-PCR or ELISA; however, these tests often have limited speed, sensitivity or specificity. Here, we demonstrate that rapid RNA FISH is a viable alternative method that could improve upon these limitations. We describe a platform beginning with software to generate RNA FISH probes both for distinguishing related strains of virus (even those different by a single base) and for capturing large numbers of strains simultaneously. Next, we present a simple fluidic device for reliably performing RNA FISH assays in an automated fashion. Finally, we describe an automated image processing pipeline to robustly identify uninfected and infected samples. Together, our results establish RNA FISH as a methodology with potential for viral point-of-care diagnostics.
authors.affiliation: Department of Bioengineering, University of Pennsylvania, Philadelphia, USA. rajlaboratory@gmail.com.
authors.forename: Sydney M
authors.initials: SM
authors.lastname: Shaffer
authors.forename: Rohan P
authors.initials: RP
authors.lastname: Joshi
authors.forename: Benjamin S
authors.initials: BS
authors.lastname: Chambers
authors.forename: David
authors.initials: D
authors.lastname: Sterken
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Biaesch
authors.forename: David J
authors.initials: DJ
authors.lastname: Gabrieli
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.forename: Kristen A
authors.initials: KA
authors.lastname: Feemster
authors.forename: Scott E
authors.initials: SE
authors.lastname: Hensley
authors.forename: David
authors.initials: D
authors.lastname: Issadore
authors.forename: Arjun
authors.initials: A
authors.lastname: Raj
mesh_terms: D000465:Algorithms; D000818:Animals; D004285:Dogs; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D061985:Madin Darby Canine Kidney Cells; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation*; D019095:Point-of-Care Systems; D012327:RNA Virus Infections / Q000175:diagnosis / Q000821:virology; D012328:RNA Viruses / Q000235:genetics / Q000302:isolation & purification; D012367:RNA, Viral / Q000032:analysis* / Q000235:genetics; D012372:ROC Curve
chemical_list: D012367:RNA, Viral