The emergence of the COVID-19 pandemics highlighted the need for rapid, accurate and massive virus detection techniques to control the circulation of infectious diseases. However, large-scale screening of the population requires a large number of trained healthcare workers and access to biomedical infrastructure. There is a pressing need for novel viral detection techniques which can achieve mass population testing with sensitive, specific and reliable readout, and that do not require specialized manpower and recourse to expensive equipment. Such monitoring modalities are particularly relevant in the context of highly infectious emerging pathogens, when no vaccine and/or therapeutic treatment are available.

We propose to address the shortcomings of current detection techniques by developing of low-cost, portable and highly-responsive screening device based on multifunctional DNA-biosensors integrated with a microfluidic platform. The system was designed and implemented for the detection of unamplified SARS-CoV-2 from saliva samples rather than nasopharyngeal swabs due to its simpler harvesting and reduced invasiveness which promotes higher acceptability rates. The samples are processed through an engineered microfluidic circuit composed of a first chamber for viral RNA extraction, a second chamber containing DNA-biosensor slides and a detection setup for fluorescence readout of DNA/RNA duplex formation in the presence of fluorescent dyes. The microfluidic platform and fluorescence microscopy setup were embedded in a versatile portable device that would allow point-of-care diagnostics. This strategy holds the potential to remove the need for biomedical personnel and expensive laboratory environment.

Optimization of the DNA-conjugated sensing surfaces resulted in attomolar detection of viral RNA copies, without cross-reactivity toward other respiratory viruses such as MERS. Several parameters influencing the density, orientation and spacing of immobilized DNA probes were carefully investigated. The current performance of the system resulted in the detection of 10 aM of SARS-CoV-2 RNA, in 10 minutes from human saliva. Further developments include the integration of alternative readout modalities, such as bioimpedance, and the application of the device to other viruses.