Rapid
and sensitive detection of SARS-CoV-2 virus genetic material
is of paramount importance to mitigate the COVID-19 pandemic outbreak
and lower the death toll. Herein, we report the design of a magnetofluorescent
bioplatform for the direct and specific detection of the viral RNA
of SARS-CoV-2 in the total RNA extracted from nasopharyngeal swabs
of COVID-19-positive patients. A higher fluorescence response was
achieved using two capture probes tethered to magnetic beads using
a biotin/streptavidin linkage, targeting two specific sites in the
ORF1a and S genes. Two horseradish peroxidase (HRP)-conjugated reporter
sequences, complementary to the loci of the S and N genes, were used
to reveal the presence of the viral RNA through the oxidation of o-phenylenediamine to fluorescent 2,3-diaminophenazine.
Under optimal conditions, the bioplatform showed high selectivity
and sensitivity and was able to detect as low as 0.01 ng of viral
RNA (1 × 103 copies/μL) with a linear dynamic
range varying from 0.01 to 3.0 ng (1 × 103 to 9 ×
107 copies/μL). The bioplatform was also able to
discriminate the SARS-CoV-2 RNA from those of other related viruses
such as hepatitis C, West Nile, measles, and non-polio viruses. Furthermore,
the developed biosensor was validated in 46 clinical samples (36 COVID-19-positive
patients and 10 COVID-19-negative subjects, as assessed with the gold
standard RT-qPCR method). Both sensitivity and specificity of the
developed method reached 100%. Finally, making such a simple and specific
method available in the field, at a primary point of care, can better
help the detection of SARS-CoV-2 infection in low-resource settings.