CO-INFECTS: A Highly Affordable, Portable, Nucleic-Acid-Based Rapid Detector of Active Respiratory Co-Infections via "Swab-to-Result" Integration

Early diagnosis of active viral co-infections of similar symptomatic pattern is critical for preventing life-threatening respiratory complications. While facilities for the same are currently available, those are either over-expensive or not amenable for deployment in resource-limited settings. We report a first of its kind isothermal colorimetric nucleic acid-based test integrated in a user-friendly, portable device, that can differentially diagnose respiratory viral infections having similar symptomatic pattern, and illustrate its performance by detecting co-infections of SARS-CoV-2 with seasonal influenza A virus from unprocessed swab sample in an extraction-free analysis mode within 45 minutes without intermediate manual steps. The test obviates the need of any complex disposable cartridge in preference to common laboratory utilities. Further, it harnesses machine learning empowered and smartphone interfaced colorimetric analysis without needing any specialized optical detector. The efficacy of the test is validated via community-adapted randomized field trials at underserved rural settings by frontline health workers, reporting sensitivity >96% and specificity > 98% in 1500 cohorts. The method in the form of three test genes with one internal control assay evidences to facilitate viral surveillance and enables diagnosing complex respiratory infections early enough in a plethora of settings ranging from general hospitals to the community centres, overcoming barriers to access of high-end facilities. Such adaptation of scientifically supreme multiplex nucleic acid based diagnostics in the framework of a simple and user friendly rapid test appears to be the future of infectious disease management in a democratized framework, eradicating the disparities in affordability and accessibility in resource-limited settings.