A new, 3D-printed, lab-on-chip system combines eRapid and SHERLOCK technologies into a single, postcard-sized system that can simultaneously detect the presence of both SARS-CoV-2 RNA and antibodies against the virus in a patient’s saliva. The detection, which takes under two hours, occurs via multiplexed electrochemical outputs.

The prototype device is described in Nature Biomedical Engineering in the paper, “A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma.

“In the early days, everyone was working on developing diagnostics that could detect either the SARS-CoV-2 virus or antibodies against it, but not both. We knew that we could successfully detect the presence of DNA and RNA molecules electrochemically, thanks to our work on Lyme disease. We decided to figure out how to multiplex that with antibody detection in order to create an all-in-one test to help track infections and fight the pandemic,” said Helena de Puig, PhD, a Wyss postdoctoral fellow.

The team chose saliva as their sample material because viral particles and antibodies can both be found there. For the SHERLOCK portion of the diagnostic, which detects the presence of SARS-CoV-2 RNA, the device needed to be able to extract, concentrate, and amplify viral RNA from a saliva sample, then mix it with CRISPR reagents and deliver the resulting solution to the eRapid chip portion for detection.

The team engineered a microfluidic system consisting of multiple reservoirs, channels, and heating elements to automatically mix and transfer substances within the prototype device. In the first chamber, saliva is combined with an enzyme that breaks open any viruses’ outer envelopes to expose their RNA. Then the sample is pumped into a reaction chamber, where it is heated and mixed with loop-mediated isothermal amplification (LAMP) reagents that amplify the viral RNA. After 30 minutes of amplification, a mixture containing SHERLOCK reagents is added to the chamber, and the sample is pumped onto an eRapid electrode.

How does the detection work? In the absence of SARS-CoV-2 genetic material in the mixture, single-stranded (ssDNA) molecules with biotin attached to them bind to peptide nucleic acid (PNA) on the electrode’s surface. The biotin then binds to a poly-HRP-streptavidin, which causes tetramethylbenzidine (TMB) to precipitate out of the liquid solution. When the solid TMB lands on the electrode, it changes its electrical conductivity. This change is detected as a difference in the amount of electrical current flowing through the electrode, indicating that the sample is free of the virus.

If any SARS-CoV-2 genetic material is present in the saliva sample, however, the Cas12a within the SHERLOCK mixture cuts it as well as the ssDNA. This cutting action separates the biotin molecule from the ssDNA, so that when the ssDNA binds to PNA, it does not trigger the series of reactions that causes the TMB to precipitate onto the electrode. Therefore, the conductivity of the electrode is unchanged, indicating a positive test result.

“The integration of the PNA-based assay with the poly-HRP-streptavidin/TMB reaction chemistry that we created for this device allowed us to detect the presence of SARS-CoV-2 with four times higher sensitivity than our original fluorescence-based SHERLOCK technology, and produced results in about the same amount of time,“ said Joshua Rainbow, PhD, a former visiting graduate student at the Wyss Institute who is now a doctoral student at the University of Bath. “It was also able to detect the presence of viral RNA with 100% accuracy.”

In parallel, the team customized the remaining three eRapid electrodes by studying them with different COVID-related antigens against which patients can develop antibodies: the S1 subunit of the Spike protein (S1), the ribosomal binding domain within that subunit (S1-RBD), and the N protein, which is present in most coronaviruses (N). If a patient’s saliva sample contains one or more of these antibodies, they bind to their partner antigens on the electrodes. A secondary antibody that is attached to biotin will then bind to the target antibody, triggering the same poly-HRP-streptavidin/TMB reaction and causing a change in the electrode’s conductivity.

The researchers tested these antibody-specific sensors using samples of human plasma from patients who had previously tested positive for SARS-CoV-2. The system was able to distinguish between antibodies against S1, S1-RBD, and N with over 95% accuracy.

“Being able to easily distinguish between different types of antibodies is hugely beneficial for determining whether patients’ immunity is due to vaccines versus infection, and tracking the strength of those different immunity levels over time,” said Sanjay Sharma Timilsina, PhD, a former postdoctoral fellow at the Wyss Institute and who is now a lead scientist at StataDX.

Finally, the team tested the combined viral RNA and antibody electrodes using saliva from SARS-CoV-2 patients. The team found that the multiplexed chips correctly identified positive and negative RNA and antibody samples with 100% accuracy, at the same time.

The prototype device’s low cost and compact design is user-friendly and minimizes the number of steps a patient needs to perform, reducing the possibility of user error. Customized cartridges could be easily manufactured to detect antigens and antibodies from different diseases, and could be fit into a reusable housing and readout device that a user would keep in their home.

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