Proteotyping SARS-CoV‑2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

Rapid
but yet sensitive, specific, and high-throughput detection
of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
in clinical samples is key to diagnose infected people and to better
control the spread of the virus. Alternative methodologies to PCR
and immunodiagnostics that would not require specific reagents are
worthy to investigate not only for fighting the COVID-19 pandemic
but also to detect other emergent pathogenic threats. Here, we propose
the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides
in nasopharyngeal swabs. We documented that the signal from the microbiota
present in such samples is low and can be overlooked when interpreting
shotgun proteomic data acquired on a restricted window of the peptidome
landscape. In this proof-of-concept study, simili nasopharyngeal swabs
spiked with different quantities of purified SARS-CoV-2 viral material
were used to develop a nanoLC–MS/MS acquisition method, which
was then successfully applied on COVID-19 clinical samples. We argue
that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein
are of utmost interest as their signal is intense and their elution
can be obtained within a 3 min window in the tested conditions. These
results pave the way for the development of time-efficient viral diagnostic
tests based on mass spectrometry.